1PT7

Crystal structure of the apo-form of the yfdW gene product of E. coli

1PT7 の概要

• エントリーDOI: 10.2210/pdb1pt7/pdb
• 関連するPDBエントリー: 1PT5
• 分子名称: Hypothetical protein yfdW, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: coa transferase, oxalate, acetyl-coa, e. coli, structural genomics, unknown function
• 由来する生物種: Escherichia coli, Shigella flexneri (,)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 97769.55

構造登録者

Gruez, A.,Roig-Zamboni, V.,Valencia, C.,Campanacci, V.,Cambillau, C. (登録日: 2003-06-23, 公開日: 2003-09-09, 最終更新日: 2024-02-14)

主引用文献

Gruez, A.,Roig-Zamboni, V.,Valencia, C.,Campanacci, V.,Cambillau, C.
The crystal structure of the Escherichia coli yfdW gene product reveals a New fold of two interlaced rings identifying a wide family of CoA transferases.
J.Biol.Chem., 278:34582-34586, 2003

PubMed Abstract: Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.

PubMed: 12844490
DOI: 10.1074/jbc.C300282200

実験手法

X-RAY DIFFRACTION (1.8 Å)